2pne: Difference between revisions

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{{Seed}}
[[Image:2pne.png|left|200px]]


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==Crystal Structure of the Snow Flea Antifreeze Protein==
The line below this paragraph, containing "STRUCTURE_2pne", creates the "Structure Box" on the page.
<StructureSection load='2pne' size='340' side='right'caption='[[2pne]], [[Resolution|resolution]] 0.98&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2pne]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hypogastrura_harveyi Hypogastrura harveyi]. The December 2009 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Antifreeze Proteins''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2009_12 10.2210/rcsb_pdb/mom_2009_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PNE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PNE FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.98&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pne OCA], [https://pdbe.org/2pne PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pne RCSB], [https://www.ebi.ac.uk/pdbsum/2pne PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pne ProSAT]</span></td></tr>
{{STRUCTURE_2pne|  PDB=2pne  |  SCENE=  }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q38PT6_9HEXA Q38PT6_9HEXA]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pn/2pne_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2pne ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Chemical protein synthesis and racemic protein crystallization were used to determine the X-ray structure of the snow flea antifreeze protein (sfAFP). Crystal formation from a racemic solution containing equal amounts of the chemically synthesized proteins d-sfAFP and l-sfAFP occurred much more readily than for l-sfAFP alone. More facile crystal formation also occurred from a quasi-racemic mixture of d-sfAFP and l-Se-sfAFP, a chemical protein analogue that contains an additional -SeCH2- moiety at one residue and thus differs slightly from the true enantiomer. Multiple wavelength anomalous dispersion (MAD) phasing from quasi-racemate crystals was then used to determine the X-ray structure of the sfAFP protein molecule. The resulting model was used to solve by molecular replacement the X-ray structure of l-sfAFP to a resolution of 0.98 A. The l-sfAFP molecule is made up of six antiparallel left-handed PPII helixes, stacked in two sets of three, to form a compact brick-like structure with one hydrophilic face and one hydrophobic face. This is a novel experimental protein structure and closely resembles a structural model proposed for sfAFP. These results illustrate the utility of total chemical synthesis combined with racemic crystallization and X-ray crystallography for determining the unknown structure of a protein.


===Crystal Structure of the Snow Flea Antifreeze Protein===
X-ray structure of snow flea antifreeze protein determined by racemic crystallization of synthetic protein enantiomers.,Pentelute BL, Gates ZP, Tereshko V, Dashnau JL, Vanderkooi JM, Kossiakoff AA, Kent SB J Am Chem Soc. 2008 Jul 30;130(30):9695-701. Epub 2008 Jul 4. PMID:18598029<ref>PMID:18598029</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2pne" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_18598029}}, adds the Publication Abstract to the page
*[[Antifreeze protein 3D structures|Antifreeze protein 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 18598029 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_18598029}}
__TOC__
 
</StructureSection>
==About this Structure==
2PNE is a 1 chain structure. The December 2009 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Antifreeze Proteins''  by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2009_12 10.2210/rcsb_pdb/mom_2009_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PNE OCA].
 
==Reference==
<ref group="xtra">PMID:18598029</ref><references group="xtra"/>
[[Category: Antifreeze Proteins]]
[[Category: Antifreeze Proteins]]
[[Category: Hypogastrura harveyi]]
[[Category: Large Structures]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Dashnau, J.]]
[[Category: Dashnau J]]
[[Category: Gates, Z P.]]
[[Category: Gates ZP]]
[[Category: Kossiakoff, A A.]]
[[Category: Kent SBH]]
[[Category: Kurutz, J.]]
[[Category: Kossiakoff AA]]
[[Category: Pentelute, B L.]]
[[Category: Kurutz J]]
[[Category: S B.H., Kent.]]
[[Category: Pentelute BL]]
[[Category: Tereshko, V.]]
[[Category: Tereshko V]]
[[Category: Vaderkooi, J M.]]
[[Category: Vaderkooi JM]]
[[Category: Antifreeze protein]]
[[Category: Chemical protein synthesis]]
[[Category: Native chemical ligation]]
 
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Retrieved from "https://proteopedia.org/2pne"